We conducted a multi-scaled Ecoregional Conservation Assessment for the Southern Rockies (~14.5M ha) and its trailing edge, the Santa Fe Subregion (~2.2M ha), Wyoming to New Mexico, USA. We included a representation analysis of Existing Vegetation Types (EVT), mature-old-growth forests (MOG), and four focal species—Canada lynx (Lynx canadensis), North American wolverine (Gulo gulo luscus), Mexican spotted owl (Strix occidentalis lucida), and northern goshawk (Accipiter gentilis)—in relation to 30 x 30 and 50 x 50 conservation targets. To integrate conservation targets with wildfire risk reduction to the built environment and climate change planning, we overlaid the location of wildfires and forest treatments in relation to the Wildland-Urban Interface (WUI) and included downscaled climate projections for a lower (RCP4.5) and higher (RCP8.5) emissions scenario. Protected areas were highly skewed toward upper elevation EVTs (most were >50% protected), underrepresented forest types (<30% protected), especially MOG (<22% protected) and riparian areas (~14% protected), and poorly represented habitat (<30%) for at least 3 of the focal species, especially in the subregion where nearly all the targets underperformed compared to the ecoregion. Most (>73%) forest thinning treatments over the past decade were >1-km from delineated WUI areas, well beyond the distance at which vegetation management can effectively reduce structure ignition risk (< 50-m from structures). Extreme heat, drought, snowpack reductions, altered timing of peak stream flows, increasing wildfires, and potential shifts in the climate niche of woodlands over conifer forests may impact forest dependent species, while declining snowpack may impact wolverine that den in upper elevations. Strategically targeting the built environment for fuel treatments would improve wildfire risk reduction and may allow for expansion of protected areas held up in controversy. Stepped-up protections for roadless areas, adoption of wilderness proposals, and greater protections for MOG and riparian forests are critical for meeting representation targets.